MeshBasedCellPopulationWithGhostNodes< DIM > Class Template Reference

#include <MeshBasedCellPopulationWithGhostNodes.hpp>

Inherits MeshBasedCellPopulation< DIM >.

Collaboration diagram for MeshBasedCellPopulationWithGhostNodes< DIM >:

Public Member Functions
	MeshBasedCellPopulationWithGhostNodes (MutableMesh< DIM, DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >(), bool deleteMesh=false, double ghostSpringStiffness=15.0)
	MeshBasedCellPopulationWithGhostNodes (MutableMesh< DIM, DIM > &rMesh, double ghostSpringStiffness=15.0)
virtual	~MeshBasedCellPopulationWithGhostNodes ()
std::set< unsigned >	GetNeighbouringLocationIndices (CellPtr pCell)
void	UpdateNodeLocations (double dt)
std::vector< bool > &	rGetGhostNodes ()
bool	IsGhostNode (unsigned index)
std::set< unsigned >	GetGhostNodeIndices ()
void	UpdateGhostPositions (double dt)
void	UpdateGhostNodesAfterReMesh (NodeMap &rMap)
c_vector< double, DIM >	CalculateForceBetweenGhostNodes (const unsigned &rNodeAGlobalIndex, const unsigned &rNodeBGlobalIndex)
CellPtr	AddCell (CellPtr pNewCell, const c_vector< double, DIM > &rCellDivisionVector, CellPtr pParentCell)
virtual void	OpenWritersFiles (OutputFileHandler &rOutputFileHandler)
virtual void	WriteVtkResultsToFile (const std::string &rDirectory)
void	OutputCellPopulationParameters (out_stream &rParamsFile)
Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
void	SetGhostNodes (const std::set< unsigned > &rGhostNodeIndices)
void	Validate ()
Private Attributes
std::vector< bool >	mIsGhostNode
double	mGhostSpringStiffness
Friends
class	TestMeshBasedCellPopulationWithGhostNodes
class	boost::serialization::access

Detailed Description

template<unsigned DIM>
class MeshBasedCellPopulationWithGhostNodes< DIM >

A facade class encapsulating a mesh-based cell population with ghost nodes.

If simulating a crypt with a mesh-based cell population, the mesh should be surrounded by at least one layer of ghost nodes. These are nodes which do not correspond to a cell, but are necessary for remeshing (because the remesher tries to create a convex hull of the set of nodes) and visualization purposes. The MeshBasedCellPopulationWithGhostNodes class deals with these ghost nodes, hiding the 'ghost nodes' concept from the OffLatticeSimulation class, so the latter only ever deals with real cells.

Definition at line 56 of file MeshBasedCellPopulationWithGhostNodes.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

MeshBasedCellPopulationWithGhostNodes< DIM >::MeshBasedCellPopulationWithGhostNodes	(	MutableMesh< DIM, DIM > &	rMesh,
		std::vector< CellPtr > &	rCells,
		const std::vector< unsigned >	locationIndices = `std::vector<unsigned>()`,
		bool	deleteMesh = `false`,
		double	ghostSpringStiffness = `15.0`
	)			`[inline]`

Create a new cell population from a mesh and collection of cells.

Parameters:

	rMesh	a mutable tetrahedral mesh
	rCells	cells corresponding to the nodes of the mesh
	locationIndices	an optional vector of location indices that correspond to real cells
	deleteMesh	set to true if you want the cell population to free the mesh memory on destruction
	ghostSpringStiffness	spring stiffness used to move the ghost nodes defaults to 15.0.

Definition at line 50 of file MeshBasedCellPopulationWithGhostNodes.cpp.

References MeshBasedCellPopulation< DIM >::GetNode(), MeshBasedCellPopulation< DIM >::GetNumNodes(), MeshBasedCellPopulationWithGhostNodes< DIM >::mIsGhostNode, MeshBasedCellPopulationWithGhostNodes< DIM >::SetGhostNodes(), and MeshBasedCellPopulationWithGhostNodes< DIM >::Validate().

template<unsigned DIM>

MeshBasedCellPopulationWithGhostNodes< DIM >::MeshBasedCellPopulationWithGhostNodes	(	MutableMesh< DIM, DIM > &	rMesh,
		double	ghostSpringStiffness = `15.0`
	)			`[inline]`

Constructor for use by the de-serializer.

Parameters:

	rMesh	a mutable tetrahedral mesh.
	ghostSpringStiffness	spring stiffness used to move the ghost nodes defaults to 15.0.

Definition at line 90 of file MeshBasedCellPopulationWithGhostNodes.cpp.

template<unsigned DIM>

MeshBasedCellPopulationWithGhostNodes< DIM >::~MeshBasedCellPopulationWithGhostNodes ( ) [inline, virtual]

Empty destructor so archiving works with static libraries.

Definition at line 98 of file MeshBasedCellPopulationWithGhostNodes.cpp.

Member Function Documentation

template<unsigned DIM>

CellPtr MeshBasedCellPopulationWithGhostNodes< DIM >::AddCell	(	CellPtr	pNewCell,
		const c_vector< double, DIM > &	rCellDivisionVector,
		CellPtr	pParentCell
	)			`[inline]`

Overridden AddCell() method.

Add a new cell to the cell population and update mIsGhostNode.

Parameters:

	pNewCell	the cell to add
	rCellDivisionVector	the position in space at which to put it
	pParentCell	pointer to a parent cell - this is required for mesh-based cell populations

Returns:: address of cell as it appears in the cell list (internal of this method uses a copy constructor along the way)

Definition at line 213 of file MeshBasedCellPopulationWithGhostNodes.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell(), MeshBasedCellPopulation< DIM >::GetNumNodes(), and MeshBasedCellPopulationWithGhostNodes< DIM >::mIsGhostNode.

template<unsigned DIM>

c_vector< double, DIM > MeshBasedCellPopulationWithGhostNodes< DIM >::CalculateForceBetweenGhostNodes	(	const unsigned &	rNodeAGlobalIndex,
		const unsigned &	rNodeBGlobalIndex
	)			`[inline]`

This method is used to calculate the force between GHOST nodes.

Parameters:

	rNodeAGlobalIndex
	rNodeBGlobalIndex

Returns:: The force exerted on Node A by Node B.

Definition at line 194 of file MeshBasedCellPopulationWithGhostNodes.cpp.

References MeshBasedCellPopulation< DIM >::GetNode(), MeshBasedCellPopulationWithGhostNodes< DIM >::mGhostSpringStiffness, and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh.

Referenced by MeshBasedCellPopulationWithGhostNodes< DIM >::UpdateGhostPositions().

template<unsigned DIM>

std::set< unsigned > MeshBasedCellPopulationWithGhostNodes< DIM >::GetGhostNodeIndices ( ) [inline]

Returns:: the indices of those nodes that are ghost nodes.

Definition at line 115 of file MeshBasedCellPopulationWithGhostNodes.cpp.

References MeshBasedCellPopulationWithGhostNodes< DIM >::mIsGhostNode.

template<unsigned DIM>

std::set< unsigned > MeshBasedCellPopulationWithGhostNodes< DIM >::GetNeighbouringLocationIndices ( CellPtr pCell ) [inline, virtual]

Overridden GetNeighbouringLocationIndices() method.

Given a cell, returns the set of location indices corresponding to neighbouring cells.

Parameters:

pCell

a cell

Returns:: the set of neighbouring location indices.

Reimplemented from AbstractCentreBasedCellPopulation< ELEMENT_DIM, ELEMENT_DIM >.

Definition at line 283 of file MeshBasedCellPopulationWithGhostNodes.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell(), MeshBasedCellPopulation< DIM >::GetNeighbouringNodeIndices(), and MeshBasedCellPopulationWithGhostNodes< DIM >::IsGhostNode().

template<unsigned DIM>

bool MeshBasedCellPopulationWithGhostNodes< DIM >::IsGhostNode ( unsigned index ) [inline, virtual]

Overridden IsGhostNode() method.

Find if a given node is a ghost node. The abstract method always returns false but is overridden in subclasses.

Parameters:

index

the global index of a specified node

Returns:: whether the node is a ghost node

Reimplemented from AbstractCentreBasedCellPopulation< ELEMENT_DIM, ELEMENT_DIM >.

Definition at line 109 of file MeshBasedCellPopulationWithGhostNodes.cpp.

References MeshBasedCellPopulationWithGhostNodes< DIM >::mIsGhostNode.

Referenced by MeshBasedCellPopulationWithGhostNodes< DIM >::GetNeighbouringLocationIndices(), and MeshBasedCellPopulationWithGhostNodes< DIM >::WriteVtkResultsToFile().

template<unsigned DIM>

void MeshBasedCellPopulationWithGhostNodes< DIM >::OpenWritersFiles ( OutputFileHandler & rOutputFileHandler ) [inline, virtual]

Overridden OpenWritersFiles() method.

Open all files in mCellPopulationWriters and mCellWriters for writing (not appending).

Parameters:

rOutputFileHandler

handler for the directory in which to open this file.

Reimplemented from MeshBasedCellPopulation< DIM >.

Definition at line 317 of file MeshBasedCellPopulationWithGhostNodes.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mOutputResultsForChasteVisualizer.

template<unsigned DIM>

void MeshBasedCellPopulationWithGhostNodes< DIM >::OutputCellPopulationParameters ( out_stream & rParamsFile ) [inline, virtual]

Outputs CellPopulation parameters to file

As this method is pure virtual, it must be overridden in subclasses.

Parameters:

rParamsFile

the file stream to which the parameters are output

Reimplemented from MeshBasedCellPopulation< DIM >.

Definition at line 406 of file MeshBasedCellPopulationWithGhostNodes.cpp.

References MeshBasedCellPopulationWithGhostNodes< DIM >::mGhostSpringStiffness.

template<unsigned DIM>

std::vector< bool > & MeshBasedCellPopulationWithGhostNodes< DIM >::rGetGhostNodes ( ) [inline]

Returns:: mIsGhostNode.

Definition at line 103 of file MeshBasedCellPopulationWithGhostNodes.cpp.

References MeshBasedCellPopulationWithGhostNodes< DIM >::mIsGhostNode.

template<unsigned DIM>

template<class Archive >

void MeshBasedCellPopulationWithGhostNodes< DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)			`[inline, private]`

Serialize the object and its member variables.

Note that serialization of the mesh and cells is handled by load/save_construct_data.

Note also that member data related to writers is not saved - output must be set up again by the caller after a restart.

Parameters:

	archive	the archive
	version	the current version of this class

Reimplemented from MeshBasedCellPopulation< DIM >.

Definition at line 85 of file MeshBasedCellPopulationWithGhostNodes.hpp.

References MeshBasedCellPopulationWithGhostNodes< DIM >::mGhostSpringStiffness, and MeshBasedCellPopulationWithGhostNodes< DIM >::mIsGhostNode.

template<unsigned DIM>

void MeshBasedCellPopulationWithGhostNodes< DIM >::SetGhostNodes ( const std::set< unsigned > & rGhostNodeIndices ) [inline, private]

Set the ghost nodes by taking in a set of which nodes indices are ghost nodes.

Parameters:

rGhostNodeIndices

set of node indices corresponding to ghost nodes

Definition at line 129 of file MeshBasedCellPopulationWithGhostNodes.cpp.

References MeshBasedCellPopulationWithGhostNodes< DIM >::mIsGhostNode, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh, and MeshBasedCellPopulationWithGhostNodes< DIM >::Validate().

Referenced by MeshBasedCellPopulationWithGhostNodes< DIM >::MeshBasedCellPopulationWithGhostNodes().

template<unsigned DIM>

void MeshBasedCellPopulationWithGhostNodes< DIM >::UpdateGhostNodesAfterReMesh ( NodeMap & rMap ) [inline, virtual]

Update mIsGhostNode if required by a remesh.

Parameters:

rMap

A map between node indices before and after remesh

Reimplemented from MeshBasedCellPopulation< DIM >.

Definition at line 262 of file MeshBasedCellPopulationWithGhostNodes.cpp.

References NodeMap::GetNewIndex(), MeshBasedCellPopulation< DIM >::GetNumNodes(), NodeMap::GetSize(), NodeMap::IsDeleted(), and MeshBasedCellPopulationWithGhostNodes< DIM >::mIsGhostNode.

template<unsigned DIM>

void MeshBasedCellPopulationWithGhostNodes< DIM >::UpdateGhostPositions ( double dt ) [inline]

Update the GhostNode positions using the spring force model with rest length=1. Forces are applied to ghost nodes from connected ghost and normal nodes.

Parameters:

dt

Definition at line 144 of file MeshBasedCellPopulationWithGhostNodes.cpp.

References MeshBasedCellPopulationWithGhostNodes< DIM >::CalculateForceBetweenGhostNodes(), AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetDampingConstantNormal(), MeshBasedCellPopulation< DIM >::GetNumNodes(), MeshBasedCellPopulationWithGhostNodes< DIM >::mIsGhostNode, and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mrMesh.

Referenced by MeshBasedCellPopulationWithGhostNodes< DIM >::UpdateNodeLocations().

template<unsigned DIM>

void MeshBasedCellPopulationWithGhostNodes< DIM >::UpdateNodeLocations ( double dt ) [inline, virtual]

Overridden UpdateNodeLocation() method.

Update the location of each node in the cell population given a time step over which to integrate the equations of motion.

Parameters:

dt

time step

Reimplemented from AbstractCentreBasedCellPopulation< ELEMENT_DIM, ELEMENT_DIM >.

Definition at line 306 of file MeshBasedCellPopulationWithGhostNodes.cpp.

References MeshBasedCellPopulationWithGhostNodes< DIM >::UpdateGhostPositions().

template<unsigned DIM>

void MeshBasedCellPopulationWithGhostNodes< DIM >::Validate ( ) [inline, private, virtual]

This is called after a cell population has been constructed to check the user gave consistent instructions. Check consistency of our internal data structures: Each node must have a cell associated with it OR must be a ghost node.

It is called after cells are added or removed from MeshBasedCellPopulation as it is an overridden virtual method.

Reimplemented from MeshBasedCellPopulation< DIM >.

Definition at line 233 of file MeshBasedCellPopulationWithGhostNodes.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End(), EXCEPTION, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell(), MeshBasedCellPopulation< DIM >::GetNumNodes(), and MeshBasedCellPopulationWithGhostNodes< DIM >::mIsGhostNode.

Referenced by MeshBasedCellPopulationWithGhostNodes< DIM >::MeshBasedCellPopulationWithGhostNodes(), and MeshBasedCellPopulationWithGhostNodes< DIM >::SetGhostNodes().

template<unsigned DIM>

void MeshBasedCellPopulationWithGhostNodes< DIM >::WriteVtkResultsToFile ( const std::string & rDirectory ) [inline, virtual]

Overridden WriteVtkResultsToFile() method.

Parameters:

rDirectory

pathname of the output directory, relative to where Chaste output is stored